SMTL ID : 5b55.1

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 17 residues within 4Å: Chain A: K.50, N.80, G.186, V.187, G.188, T.189, G.190, G.191, T.192, E.232, G.233, I.234, S.276, P.302, D.303, Y.308 Ligands: 0JO.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.50 Hydrogen bonds: A:K.50, A:G.188, A:T.189, A:G.190, A:G.191, A:T.192, A:T.192, A:T.192, A:S.276 Water bridges: A:N.80, A:N.157, A:N.157, A:V.193, A:N.280 Salt bridges: A:K.50 PLP.4: 17 residues within 4Å: Chain B: K.50, N.80, G.186, V.187, G.188, T.189, G.190, G.191, T.192, E.232, G.233, I.234, S.276, P.302, D.303, Y.308 Ligands: 0JO.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.50 Hydrogen bonds: B:N.80, B:G.188, B:T.189, B:G.190, B:G.191, B:T.192, B:T.192, B:S.276 Water bridges: B:K.50, B:K.50, B:N.80, B:H.161, B:T.189, B:V.193 Salt bridges: B:K.50

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.2: 23 residues within 4Å: Chain A: K.50, T.77, S.78, G.79, N.80, T.81, Q.151, G.186, V.187, G.188, T.189, G.190, G.191, T.192, E.232, G.233, I.234, N.236, S.276, P.302, D.303, Y.308 Ligands: PLP.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.189, A:I.234, A:P.302 Hydrogen bonds: A:K.50, A:T.77, A:S.78, A:S.78, A:G.79, A:N.80, A:T.81, A:Q.151, A:G.188, A:T.189, A:G.190, A:G.191, A:T.192, A:T.192, A:T.192, A:S.276 Water bridges: A:N.157, A:N.157, A:V.193, A:N.280 Salt bridges: A:K.50, A:K.50 0JO.5: 23 residues within 4Å: Chain B: K.50, T.77, S.78, G.79, N.80, T.81, Q.151, G.186, V.187, G.188, T.189, G.190, G.191, T.192, E.232, G.233, I.234, N.236, S.276, P.302, D.303, Y.308 Ligands: PLP.4 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.189, B:I.234, B:P.302 Hydrogen bonds: B:S.78, B:S.78, B:G.79, B:N.80, B:N.80, B:T.81, B:T.81, B:Q.151, B:Q.151, B:G.188, B:T.189, B:G.190, B:G.191, B:T.192, B:T.192, B:S.276 Water bridges: B:K.50, B:R.108, B:N.157, B:T.189, B:T.192, B:V.193 Salt bridges: B:K.50, B:K.50

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: K.331, E.332 Chain B: K.9, A.90, I.91, G.93 No protein-ligand interaction detected (PLIP) PEG.6: 6 residues within 4Å: Chain B: E.14, K.19, Y.56, Y.163, G.164, E.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.168 Water bridges: B:E.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kezuka, Y. et al., Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen sulfide-producing oral pathogen,Fusobacterium nucleatum. Biochem. J. (2018)

Release Date

2017-04-26

Peptides

Cysteine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cysteine synthase